Image analysis programs developed in our laboratory by Dr. David Mastronarde have been used to give reliable views of both inner and outer dynein arms found on the doublet microtubules of Chlamydomonas flagella (Mastronarde et al., 1992). We have used these programs to compare the inner dynein arms from wild type flagella with those from several mutants with altered flagellar function and known biochemical defects. This correlative biochemical and structural approach has been used to study dynein organization in a number of mutant strains of Chlamydomonas (Gardner et al., 1994; King et al., 1994). There has been increased interest in the scientific community to learn the technology developed in our laboratory. We have written a detailed chapter in the Methods in Cell Biology series describing image analysis programs and procedures (O'Toole et al., 1995). In addition, we have had a graduate student visit our lab for a week to learn the programs and the steps involved, from taking an appropriate image on the microscope through image averaging and statistical analysis. We have written two manuals describing the details of all programs used in the image analysis as well as a step-by-step procedure to obtain both cross section and longitudinal averages. We are also in the process of converting the programs to run on UNIX machines to increase the flexibility of the technology to the scientific community.